Ab initio (UHF/6-31G*) and density functional (Becke3LYP/D95*) calculations have been used to investigate the structures and stabilities of the radical cations of the DNA bases and base pairs. The calculated structures of the base pairs show excellent agreement with crystallographic data. The most easily oxidizable base, guanine, forms a particularly stable radical cation base pair with cytosine, so that the calculated adiabatic ionization potential for the guanine-cytosine hydrogen-bonded complex is about 0.75 eV lower than that of guanine itself. UBecke3LYP/D95*//UHF/6-31G* calculations show that the shift of the central hydrogen-bonded proton at N1 of guanine to N3 of cytosine is only slightly endothermic (+1.6 kcal mol -1 ). The product of the corresponding proton shift in the adenine-thymine system is unfavorable by +14.1 kcal mol -1 . These results suggest that the guaninecytosine radical cation represents even more of a thermodynamic sink in oxidized DNA than might be concluded from the ionization potentials of the individual bases, and that it enjoys about 7.3 kcal mol -1 extra stabilization from the central low-barrier hydrogen bond.

We present a molecular dynamics study of cytochrome c oxidase from Paracoccus denitrificans in the fully oxidized state, embedded in a fully hydrated dimyristoylphosphatidylcholine lipid bilayer membrane. Parallel simulations with different levels of protein hydration, 1.125 ns each in length, were carried out under conditions of constant temperature and pressure using three-dimensional periodic boundary conditions and full electrostatics to investigate the distribution and dynamics of water molecules and their corresponding hydrogen-bonded networks inside cytochrome c oxidase. The majority of the water molecules had residence times shorter than 100 ps, but a few water molecules are fixed inside the protein for up to 1.125 ns. The hydrogen-bonded network in cytochrome c oxidase is not uniformly distributed, and the degree of water arrangement is variable. The average number of solvent sites in the proton-conducting K- and D-pathways was determined. In contrast to single water files in narrow geometries we observe significant diffusion of individual water molecules along these pathways. The highly fluctuating hydrogen-bonded networks, combined with the significant diffusion of individual water molecules, provide a basis for the transfer of protons in cytochrome c oxidase, therefore leading to a better understanding of the mechanism of proton pumping.

Time-resolved FTIR spectroscopic studies of the flash photolysis of several 1-(2-nitrophenyl)ethyl ethers derived from aliphatic alcohols showed that a long-lived hemiacetal intermediate was formed during the reaction. Breakdown of this intermediate was rate-limiting for product release. One of these compounds (methyl 2-[1-(2-nitrophenyl)ethoxy]ethyl phosphate, 9) was studied in detail by a combination of time-resolved FTIR and UV-vis spectroscopy. In addition, product studies confirmed clean photolytic decomposition to the expected alcohol, 2-hydroxyethyl methyl phosphate, and the 2-nitrosoacetophenone byproduct. At pH 7.0, 1 degrees C, the rate constant for product release was 0.11 s(-1), very much slower than the 5020 s(-1) rate constant for decay of the photochemically generated aci-nitro intermediate (pH 7.0, 2 degrees C). Time-resolved UV-vis measurements showed that the hemiacetal intermediate is formed by two competing pathways, with fast (approximately 80% of the reaction flux) and slow (approximately 20% of the flux) components. Only the minor, slower path is responsible for the observed aci-nitro decay process. These competing reactions are interpreted with the aid of semiempirical PM3 calculations of reaction barriers. Furthermore, AMSOL calculations indicate that the pK(a) of the nitronic acid isomer formed by photolysis is likely to determine partition into the alternate paths. These unusual results appear to be general for 1-(2-nitrophenyl)ethyl ethers and contrast with a related 2-nitrobenzyl ether that photolyzed without involvement of a long-lived hemiacetal.

Phospholamban (PLN) is an intrinsic membrane protein of 52 amino acids that modulates the activity of the reticular Ca 2 ion pump. We recently solved the three-dimensional structure of chemically synthesized, unphosphorylated, monomeric PLN (C41F) by high-resolution nuclear magnetic resonance spectroscopy in chloroform/methanol. The structure is composed of two a-helical regions connected by a b turn (Type III). We used this structure and the crystallographic structure of the sarcoplasmic reticulum calcium pump (SERCA) recently determined by Toyoshima and co-workers and modeled into its E 2 form by Stokes (1KJU) or by Toyoshima (1FQU). We applied restrained and unrestrained energy optimizations and used the AMBER molecular mechanics force field to model the complex formed between PLN and the pump. The results indicate that transmembrane helix 6 (M6) of the SERCA pump is energetically favored, with respect to the other transmembrane helices, as the PLN binding partner within the membrane and is the only one of these helices that also permits contact between the N-terminal residues of PLN and the critical cytosolic binding loop region of the pump. This result is in agreement with published biochemical data and with the predictions of previous mutagenesis work on the membrane sector of the pump. The model reveals that PLN does not span the entire width of the membrane, that is, its hydrophobic C-terminal end is located near the center of the transmembrane region of the SERCA pump. The model also shows that interaction with M6 is stabilized by additional contacts made by PLN to M4. The contact between the N-terminal portion of PLN and the pump is stabilized by a number of salt and hydrogen-bond bridges, which may be abolished by phosphorylation of PLN. The contacts between the cytosolic portions of PLN and the pump are only observed in the E 2 conformation of the pump. Our model of the complex also offers a plausible structural explanation for the preference of protein kinase A for phosphorylation of Ser16 of PLN.

A computational approach to quantify the druglike character of chemical compounds is presented. For this purpose, the distribution of atom types and their pair-wise combinations in known drugs and nondrugs was examined. Statistical analysis of the occurrence probabilities was used to derive a drug-likeliness score on a logarithmic scale. "Typical" pharmaceutical agents exhibit scores greater than 0.3, while for ordinary substances, values below 0 are expected. Although any kind of fitting or error minimization scheme is absent in this method, confirmed drugs are predicted with an accuracy of at least 71%. Many falsely predicted nondrugs were found to closely resemble actual drugs or to contain unsuitable substitution patterns that can easily be ruled out by applying medicinal knowledge. As the outlined method is computationally inexpensive, this drug-likeliness score can therefore be used as a filter for the in silico screening of large substance databases.

Ab initio and other computational studies of bacterial reaction center cofactors are usually performed using the observed (low-resolution) X-ray structures. Unfortunately, these geometries are necessarily approximate and this can have dramatic influences on calculated properties. For example, the calculated energies of the four bacteriochlorophylls in Rhodobacter sphaeroides vary by over 160 kcal mol-1. To overcome this problem, a combined quantum mechanical/molecular mechanical (QM/MM) method is employed to optimize the structure of the special pair and other cofactors in the photosynthetic reaction centers of Rhodopseudomonas viridis and Rhodobacter sphaeroides, while a purely MM model is used to refine the structure of the remaining protein environment. Specifically, the QM/MM optimizations are performed using a semiempirical AM1-based formalism. After relaxation, the energies of the bacteriochlorophylls differ by only typical conformer relative energies, ca. 5 kcal mol-1. Another example of improved cofactor properties is the PL−PM interaction energy which has been predicted to be strongly repulsive at the X-ray structure but here is shown to be realistically attractive after optimization. After optimization, the distortions in the geometries of the cofactor are seen to be controlled by protein−cofactor interactions, and the cofactors on the L-side are all seen to fit more snugly together within the protein environment than do their M-side counterparts. Also, the 2a-acetyl group of PM for Rb. sphaeroides, for which hydrogen bonding to the protein is restricted, is predicted to form a weakly bound sixth ligand to the magnesium of PL; this is consistent with, but not obvious from, the X-ray structure.

Magnesium parameters for use with the semiempirical AM1 method are developed using a specially designed genetic algorithm. Parametrization priorities included development of a robust parametrization capable of describing a wide range of properties in diverse chemical environments, with emphasis on structural features of biologically relevant systems, e.g., chlorophylls. Specifically, the test data set included a selection of the heats of formation, geometric properties, dipole moment, and ionization energies evaluated for 32 compounds including halides, oxides, hypervalent compounds, organometallics, and porphyrins. In addition, calculated properties for an additional 27 molecules are used as an independent test on the quality of the parametrization obtained. Reference data are taken from eitherexperiment or previous ab initio calculations or evaluated using ab initio or density functional theory. For comparison, analogous results for all 59 molecules are obtained using the semiempirical PM3 and MNDO/d methods. Both AM1 and MNDO/d are found to be robust and widely applicable for magnesium compounds while the applicability of PM3 appears significantly restricted. MNDO/d appears the method of choice for ionization potentials and heats of formation while, reflecting our parametrization priorities, AM1 appears the method of choice for geometrical properties, especially those of magnesium porphyrins.

Sesquiterpenes are particularly interesting as flavorings and fragrances or as pharmaceuticals. Regio- or stereoselective functionalizations of terpenes are one of the main goals of synthetic organic chemistry, which are possible through radical reactions but are not selective enough to introduce the desired chiral alcohol function into those compounds. Cytochrome P450 monooxygenases are versatile biocatalysts and are capable of performing selective oxidations of organic molecules. We were able to demonstrate that CYP109D1 from Sorangium cellulosum So ce56 functions as a biocatalyst for the highly regioselective hydroxylation of norisoprenoids, alpha- and beta-ionone, which are important aroma compounds of floral scents. The substrates alpha- and beta-ionone were regioselectively hydroxylated to 3-hydroxy-alpha-ionone and 4-hydroxy-beta-ionone, respectively, which was confirmed by (1)H NMR and (13)C NMR. The results of docking alpha- and beta-ionone into a homology model of CYP109D1 gave a rational explanation for the regio-selectivity of the hydroxylation. Kinetic studies revealed that alpha- and beta-ionone can be hydroxylated with nearly identical V (max) and K (m) values. This is the first comprehensive investigation of the regioselective hydroxylation of norisoprenoids by CYP109D1.